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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genoCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genoCN_1.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoCN’ version ‘1.58.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genoCN’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genoCNA: no visible binding for global variable ‘init.Para.CNA’
genoCNV: no visible binding for global variable ‘init.Para.CNV’
Undefined global functions or variables:
  init.Para.CNA init.Para.CNV
* checking Rd files ... NOTE
checkRd: (-1) genoCNA.Rd:60: Escaped LaTeX specials: \_
checkRd: (-1) genoCNA.Rd:61: Escaped LaTeX specials: \_
checkRd: (-1) genoCNV.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) init.Para.CNA.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNA.Rd:42-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.Para.CNV.Rd:42-46: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/genoCN.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genoCN
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tnorm_mle.c -o tnorm_mle.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utility.c -o utility.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c xCNV.c -o xCNV.o
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
  int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
               ^
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
  int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                        ^
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
  int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
         ^
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
  double mu_b_tmp, sd_b_tmp;
         ^
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
  double mu_b_tmp, sd_b_tmp;
                   ^
5 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-genoCN/00new/genoCN/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoCN)